1. Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York 10021, USA
2. Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York 10021, USA
3. Verna and Marrs McLean Department of Biochemistry and Molecular Biology, and Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA
4. Department of Pathology and Kaplan Comprehensive Cancer Center, NYU Medical Center, New York 10016, USA
5. Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
6. Present address: Departments of Structural Biology and Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.

Correspondence to: Nikola P. Pavletich^1,2 Correspondence and requests for materials should be addressed to N.P.P. (e-mail: Email: nikola@xray2.mskcc.org). Coordinates have been deposited with the Protein Data Bank under accession codes 1LDD, 1LDJ and 1LDK.

Abstract

SCF complexes are the largest family of E3 ubiquitin–protein ligases and mediate the ubiquitination of diverse regulatory and signalling proteins. Here we present the crystal structure of the Cul1–Rbx1–Skp1–F box^Skp2 SCF complex, which shows that Cul1 is an elongated protein that consists of a long stalk and a globular domain. The globular domain binds the RING finger protein Rbx1 through an intermolecular -sheet, forming a two-subunit catalytic core that recruits the ubiquitin-conjugating enzyme. The long stalk, which consists of three repeats of a novel five-helix motif, binds the Skp1–F box^Skp2 protein substrate-recognition complex at its tip. Cul1 serves as a rigid scaffold that organizes the Skp1–F box^Skp2 and Rbx1 subunits, holding them over 100 Å apart. The structure suggests that Cul1 may contribute to catalysis through the positioning of the substrate and the ubiquitin-conjugating enzyme, and this model is supported by Cul1 mutations designed to eliminate the rigidity of the scaffold.